AMR/R/disk.R

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# ==================================================================== #
# TITLE #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
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# Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many #
# colleagues from around the world, see our website. #
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# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
#' Transform Input to Disk Diffusion Diameters
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#'
#' This transforms a vector to a new class [`disk`], which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 6 and 50.
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#' @rdname as.disk
#' @param x vector
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#' @param na.rm a [logical] indicating whether missing values should be removed
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#' @details Interpret disk values as SIR values with [as.sir()]. It supports guidelines from EUCAST and CLSI.
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#'
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#' Disk diffusion growth zone sizes must be between 6 and 50 millimetres. Values higher than 50 but lower than 100 will be maximised to 50. All others input values outside the 6-50 range will return `NA`.
#' @return An [integer] with additional class [`disk`]
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#' @aliases disk
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#' @export
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#' @seealso [as.sir()]
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#' @examples
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#' # transform existing disk zones to the `disk` class (using base R)
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#' df <- data.frame(
#' microorganism = "Escherichia coli",
#' AMP = 20,
#' CIP = 14,
#' GEN = 18,
#' TOB = 16
#' )
#' df[, 2:5] <- lapply(df[, 2:5], as.disk)
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#' str(df)
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#'
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#' \donttest{
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#' # transforming is easier with dplyr:
#' if (require("dplyr")) {
#' df %>% mutate(across(AMP:TOB, as.disk))
#' }
#' }
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#'
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#' # interpret disk values, see ?as.sir
#' as.sir(
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#' x = as.disk(18),
#' mo = "Strep pneu", # `mo` will be coerced with as.mo()
#' ab = "ampicillin", # and `ab` with as.ab()
#' guideline = "EUCAST"
#' )
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#'
#' # interpret whole data set, pretend to be all from urinary tract infections:
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#' as.sir(df, uti = TRUE)
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as.disk <- function(x, na.rm = FALSE) {
meet_criteria(x, allow_class = c("disk", "character", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(na.rm, allow_class = "logical", has_length = 1)
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if (!is.disk(x)) {
x <- unlist(x)
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if (isTRUE(na.rm)) {
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x <- x[!is.na(x)]
}
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x[trimws2(x) == ""] <- NA
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x.bak <- x
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na_before <- length(x[is.na(x)])
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# heavily based on cleaner::clean_double():
clean_double2 <- function(x, remove = "[^0-9.,-]", fixed = FALSE) {
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x <- gsub(",", ".", x, fixed = TRUE)
# remove ending dot/comma
x <- gsub("[,.]$", "", x)
# only keep last dot/comma
reverse <- function(x) vapply(FUN.VALUE = character(1), lapply(strsplit(x, NULL), rev), paste, collapse = "")
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x <- sub("{{dot}}", ".",
gsub(".", "",
reverse(sub(".", "}}tod{{",
reverse(x),
fixed = TRUE
)),
fixed = TRUE
),
fixed = TRUE
)
x_clean <- gsub(remove, "", x, ignore.case = TRUE, fixed = fixed)
# remove everything that is not a number or dot
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as.double(gsub("[^0-9.]+", "", x_clean))
}
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# round up and make it an integer
x <- as.integer(ceiling(clean_double2(x)))
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# disks can never be less than 6 mm (size of smallest disk) or more than 50 mm
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x[x < 6 | x > 99] <- NA_integer_
x[x > 50] <- 50L
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na_after <- length(x[is.na(x)])
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if (na_before != na_after) {
list_missing <- x.bak[is.na(x) & !is.na(x.bak)] %pm>%
unique() %pm>%
sort() %pm>%
vector_and(quotes = TRUE)
cur_col <- get_current_column()
warning_("in `as.disk()`: ", na_after - na_before, " result",
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ifelse(na_after - na_before > 1, "s", ""),
ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
" truncated (",
round(((na_after - na_before) / length(x)) * 100),
"%) that were invalid disk zones: ",
list_missing,
call = FALSE
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)
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}
}
set_clean_class(as.integer(x),
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new_class = c("disk", "integer")
)
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}
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all_valid_disks <- function(x) {
if (!inherits(x, c("disk", "character", "numeric", "integer"))) {
return(FALSE)
}
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x_disk <- tryCatch(suppressWarnings(as.disk(x[!is.na(x)])),
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error = function(e) NA
)
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!anyNA(x_disk) && !all(is.na(x))
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}
#' @rdname as.disk
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#' @details `NA_disk_` is a missing value of the new `disk` class.
#' @export
NA_disk_ <- set_clean_class(as.integer(NA_real_),
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new_class = c("disk", "integer")
)
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#' @rdname as.disk
#' @export
is.disk <- function(x) {
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inherits(x, "disk")
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}
# will be exported using s3_register() in R/zzz.R
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pillar_shaft.disk <- function(x, ...) {
out <- trimws(format(x))
out[is.na(x)] <- font_na(NA)
create_pillar_column(out, align = "right", width = 2)
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}
# will be exported using s3_register() in R/zzz.R
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type_sum.disk <- function(x, ...) {
"disk"
}
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#' @method print disk
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#' @export
#' @noRd
print.disk <- function(x, ...) {
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cat("Class 'disk'\n")
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print(as.integer(x), quote = FALSE)
}
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#' @method [ disk
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#' @export
#' @noRd
"[.disk" <- function(x, ...) {
y <- NextMethod()
attributes(y) <- attributes(x)
y
}
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#' @method [[ disk
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#' @export
#' @noRd
"[[.disk" <- function(x, ...) {
y <- NextMethod()
attributes(y) <- attributes(x)
y
}
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#' @method [<- disk
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#' @export
#' @noRd
"[<-.disk" <- function(i, j, ..., value) {
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value <- as.disk(value)
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y <- NextMethod()
attributes(y) <- attributes(i)
y
}
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#' @method [[<- disk
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#' @export
#' @noRd
"[[<-.disk" <- function(i, j, ..., value) {
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value <- as.disk(value)
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y <- NextMethod()
attributes(y) <- attributes(i)
y
}
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#' @method c disk
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#' @export
#' @noRd
c.disk <- function(...) {
as.disk(unlist(lapply(list(...), as.character)))
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}
#' @method unique disk
#' @export
#' @noRd
unique.disk <- function(x, incomparables = FALSE, ...) {
y <- NextMethod()
attributes(y) <- attributes(x)
y
}
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#' @method rep disk
#' @export
#' @noRd
rep.disk <- function(x, ...) {
y <- NextMethod()
attributes(y) <- attributes(x)
y
}
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# will be exported using s3_register() in R/zzz.R
get_skimmers.disk <- function(column) {
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skimr::sfl(
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skim_type = "disk",
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min = ~ min(as.double(.), na.rm = TRUE),
max = ~ max(as.double(.), na.rm = TRUE),
median = ~ stats::median(as.double(.), na.rm = TRUE),
n_unique = ~ length(unique(stats::na.omit(.))),
hist = ~ skimr::inline_hist(stats::na.omit(as.double(.)))
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)
}